Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
☆254Jul 24, 2026Updated this week
Alternatives and similar repositories for treetime
Users that are interested in treetime are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Ultrafast Sample Placement on Existing Trees☆140Jun 1, 2026Updated last month
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆221Aug 27, 2025Updated 10 months ago
- Estimating time trees from very large phylogenies☆28Jul 21, 2024Updated 2 years ago
- An updated pipeline for pangenome investigation☆367Jul 2, 2026Updated 3 weeks ago
- IQ-TREE software version 2: phylogenetics by maximum likelihood☆334Updated this week
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- A collection of documented examples using TreeTime☆22Jul 30, 2019Updated 6 years ago
- snipit: summarise snps relative to your reference sequence☆178Jan 13, 2026Updated 6 months ago
- Reconstruction of transmission trees using genomic data☆72Jul 14, 2026Updated last week
- Finds SNP sites from a multi-FASTA alignment file☆278Dec 16, 2020Updated 5 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated last year
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆128Jul 6, 2026Updated 2 weeks ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆124Jun 2, 2026Updated last month
- RAxML Next Generation: faster, easier-to-use and more flexible☆472Jul 6, 2026Updated 2 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- Parallel/Homoplasic SNP Finder☆20May 3, 2023Updated 3 years ago
- Pipeline components for real-time phylodynamic analysis☆277Updated this week
- A tool for exploring large trees in the browser☆133Jul 15, 2026Updated last week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated last month
- Rapid determination of appropriate reference genomes.☆102Jan 22, 2025Updated last year
- The ARTIC fieldbioinformatics pipeline☆134Jul 16, 2026Updated last week
- Scalable relaxed clock phylogenetic dating☆28Jul 5, 2026Updated 2 weeks ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Processing pipeline for pan-genome visulization and exploration☆146Oct 9, 2023Updated 2 years ago
- Finding regions of similarity between plasmids☆17Jul 15, 2026Updated last week
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated last month
- A toolbox for pangenome analysis and threshold evaluation.☆101Jul 8, 2022Updated 4 years ago
- Gotree: a set of command line tools and an API to manipulate phylogenetic trees.☆150Jul 15, 2026Updated last week
- A new high-resolution long-read metagenome assembler for even noisy reads☆157Jul 3, 2026Updated 3 weeks ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆664Jul 10, 2026Updated 2 weeks ago
- A tool to identify and annotate homoplasies on a phylogeny and sequence alignment☆24Jun 2, 2021Updated 5 years ago
- ☆18Jun 11, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Software package for assigning SARS-CoV-2 genome sequences to global lineages.☆454Jun 10, 2026Updated last month
- Reorients assembled microbial sequences☆143Jun 30, 2026Updated 3 weeks ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated last year
- Bifrost graph gene caller.☆98Jun 18, 2026Updated last month
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆260Updated this week
- Rapid haploid variant calling and core genome alignment☆594Dec 12, 2025Updated 7 months ago
- Scan contig files against PubMLST typing schemes☆294Jun 17, 2026Updated last month